The following quick start briefly summarizes the necessary steps to use our pipeline:

1. Install the necessary tools (Snakemake, samtools, and bedtools). We recommend installing them via conda, in which case the installation is as easy as

1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as

``conda install -c bioconda snakemake bedtools samtools``

``conda install -c bioconda snakemake bedtools samtools subread``

If conda is not yet installed, follow the [installation instructions](https://conda.io/docs/user-guide/install/index.html). If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: [snakemake](http://snakemake.readthedocs.io/en/stable/getting_started/installation.html), [samtools](http://www.htslib.org/download/), [bedtools](http://bedtools.readthedocs.io/en/latest/content/installation.html).

If conda is not yet installed, follow the [installation instructions](https://conda.io/docs/user-guide/install/index.html). If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: [snakemake](http://snakemake.readthedocs.io/en/stable/getting_started/installation.html), [samtools](http://www.htslib.org/download/), [bedtools](http://bedtools.readthedocs.io/en/latest/content/installation.html), [Subread](http://subread.sourceforge.net/).